Nucleic acid amplification processes

ABSTRACT

Disclosed is a method of performing a non-isothermal nucleic acid amplification reaction, the method comprising the steps of: (a) mixing a target sequence with one or more complementary single stranded primers in conditions which permit a hybridisation event in which the primers hybridise to the target, which hybridisation event, directly or indirectly, leads to the formation of a duplex structure comprising two nicking sites disposed at or near opposite ends of the duplex; and performing an amplification process by; (b) causing a nick at each of said nicking sites in the strands of the duplex; (c) using a polymerase to extend the nicked strands so as to form newly synthesised nucleic acid, which extension with the polymerase recreates nicking sites; (d) repeating steps (b) and (c) as desired so as to cause the production of multiple copies of the newly synthesised nucleic acid; characterised in that the temperature at which the method is performed is non-isothermal, and subject to a reduction of at least 2° C. during the amplification process of steps (b)-(d).

RELATED APPLICATIONS

The present application is a continuation application of U.S. patentapplication Ser. No. 16/313,750, filed Dec. 27, 2018, issued as U.S.Pat. No. 11,591,643 on Feb. 28, 2023, which is a National Stage Entry ofInternational Application No. PCT/GB2017/051927, filed Jun. 30, 2017,which claims priority to G.B. Application No. 1611469.6, filed Jun. 30,2016.

SEQUENCE LISTING

This application contains a Sequence Listing XML in computer readableform. The computer readable form is incorporated herein by reference.Said XML copy, created on Jun. 5, 2023, is named “LDX-018WOC1-SLXML.txt” and is 911,355 bytes in size.

FIELD OF THE INVENTION

The present invention relates to a method of amplifying a nucleic acid,and apparatus for performing the method.

BACKGROUND OF THE INVENTION

The polymerase chain reaction (PCR) was the first widely-used in vitromethod for the amplification of DNA. Although extremely powerful, thetechnique requires the use of thermal cycling apparatus to subject thereaction mixture to periodic temperature changes in order to effectamplification. Accordingly PCR is not especially suitable for useoutside a laboratory setting, for example in the context of apoint-of-care (“PoC”) diagnostic device.

Partly to overcome this disadvantage, numerous different isothermalamplification techniques were devised, which avoided the need forthermal cycling. Such techniques include, for example: signal mediatedamplification of RNA technology (“SMART”; WO 99/037805); nucleic acidsequence based amplification (“NASBA” Compton 1991 Nature 350. 91-92);rolling circle amplification (“RCA” e.g. see Lizardi et al., 1998 NatureGenetics 19, 225-232); loop-mediated amplification (“LAMP” see Notomi etal., 2000 Nucl. Acids Res. 28 (12) e63); recombinase polymeraseamplification (“RPA” see Piepenberg et al., 2006 PLoS Biology 4 (7)e204); strand displacement amplification (“SDA”); helicase-dependentamplification (“HDA” Vincent et al., 2004 EMBO Rep. 2, 795-800):transcription mediated amplification (“TMA”), single primer isothermalamplification (“SPTA” see Kum et al., 2005 Clinical Chemistry 51.,1973-81); self-sustained sequence replication (“3SR”); and nickingenzyme amplification reaction (“NEAR”).

SDA is a technique (disclosed by Walker et al., 1992 Nucl. Acids Res.20, 1691-1696) which involves the use of a pair of short “bumper”primers upstream to a pair of primers comprising a target-complementaryportion and, 5′ of the target-complementary portion, a recognition andcutting site for an endonuclease. The “bumper” primers help to initiatethe SDA reaction by generating complementary single stranded target forprimer amplification. The primers hybridise to respective complementarysingle stranded target molecules. The 3′ end of the target strands areextended using a reaction mix including a DNA polymerase and at leastone modified nucleotide triphosphate, using the primer as template (andlikewise, the 3′ ends of the primers are extended using the target astemplate).

The extension of the target strands generates a double strandedrecognition site for the endonuclease. However, because the target isextended using a modified triphosphate, the endonuclease does not cleaveboth strands but instead makes a single stranded nick in the primer. The3′ ends at the nicks are then extended by the DNA polymerase (typicallyKlenow fragment of DNA polymerase I, which lacks an exonucleaseactivity). As the nicked primers are extended, they displace theinitially-produced extension product. The displaced product is then freeto hybridise to the opposite primer, since it essentially replicates thesequence of the target for the opposite primer. In this way, exponentialamplification of both strands of the target sequence is achieved.

The amplification stage of the SDA process is essentiallyisothermal—typically performed at 37° C.—the optimum temperature for theendonuclease and the polymerase. However, before reaching theamplification stage it is necessary to completely dissociate the doublestranded target into its constituent single strands, in order to allowthe pair of primers to hybridise to their complementary target strands.

This dissociation, or “melting” is normally accomplished by heating thedouble stranded target to a high temperature—usually about 90° C.—inorder to break the hydrogen bonds between the two strands of the target.The reaction mix is then cooled to allow the addition of the enzymeswhich are necessary for the amplification reaction. Because of the hightemperature used to generate the single stranded targets, the SDAtechnique is not ideally suited to a PoC context.

U.S. Pat. No. 6,191,267 discloses the cloning and expression of N.BstNBInicking enzyme and its use in SDA, in place of restriction endonucleasesand modified triphosphates.

Another amplification technique, which 1s similar to SDA, is NickingEnzyme Amplification Reaction (or “NEAR”).

In ‘NEAR’ (e.g. as disclosed in US2009/0017453 and EP 2,181,196),forward and reverse primers (referred to in US 2009/0017453 and EP2,181,196 as “templates”) hybridise to respective strands of a doublestranded target and are extended. Further copies of the forward andreverse primers (present in excess) hybridise to the extension productof the opposite primer and are themselves extended, creating an“amplification duplex”. Each amplification duplex so formed comprises anicking site towards the 5′ end of each strand, which is nicked by anicking enzyme, allowing the synthesis of further extension products.The previously synthesised extension products can meanwhile hybridisewith further copies of the complementary primers, causing the primers tobe extended and thereby creating further copies of the “amplificationduplex”. In this way, exponential amplification can be achieved.

NEAR differs from SDA, in particular, in that no “bumper” primers andinitial thermal dissociation step is required. The initial primer/targethybridisation event needed to trigger the amplification process takesplace whilst the target is still substantially double stranded: it isthought that the initial primer/target hybridisation takes advantage oflocalised dissociation of the target strands—a phenomenon known as“breathing” (see Alexandrov et al., 2012 Nucl. Acids Res. and review byVon Rippel et al., 2013 Biopolymers 99 (12), 923-954). Breathing is thelocalised and transient loosening of the base pairing between strands ofDNA. The melting temperature (Tm) of the initial primer/targetheteroduplex is typically much lower than the reaction temperature, sothe tendency is for the primer to dissociate, but transienthybridisation lasts long enough for the polymerase to extend the primer,which increases the Tm of the heteroduplex, and stabilises it.

The amplification stage in NEAR is performed isothermally, at a constanttemperature. Indeed, it is conventional to perform both the initialtarget/primer hybridisation, and the subsequent amplification rounds, atthe same constant temperature, usually in the range 54 to 56° C.

Avoiding the need for thermal cycling means that isothermal techniquesare potentially more useful than PCR in PoC contexts. In addition,synthesis of significant amounts of amplification product, even whenstarting from a very low copy number of target molecules (e.g. as few as10 double stranded target molecules), can be achieved.

WO 2011/030145 (Enigma Diagnostics Limited) discloses an “isothermal”nucleic acid amplification reaction performed under conditions of atemperature oscillation, in which a reaction is performed initially at apredetermined temperature, the temperature is allowed to deviate up ordown from the predetermined temperature, and then causing thetemperature to return to the predetermined temperature at least onceduring the amplification reaction. More typically the temperature isallowed to “wobble” by a small amount (about 5° C.) up and down from thepredetermined temperature.

The present invention aims to provide, inter alia, an improved nucleicacid amplification technique having one or more advantages over existingtechniques including, for example, decreased reaction time, and/orincreased yield and/or decreased non-specific amplification products.

SUMMARY OF THE INVENTION

In a first aspect, the invention provides a method of performing anon-isothermal nucleic acid amplification reaction, the methodcomprising the steps of:

-   -   (a) mixing a target sequence with one or more complementary        single stranded primers in conditions which permit a        hybridisation event in which the primers hybridise to the        target, which hybridisation event, directly or indirectly, leads        to the formation of a duplex structure comprising two nicking        sites disposed at or near opposite ends of the duplex; and        performing an amplification process by;    -   (b) causing a nick at each of said nicking sites in the strands        of the duplex    -   (c) using a polymerase to extend the nicked strands so as to        form newly synthesised nucleic acid, which extension with the        polymerase recreates said nicking sites;    -   (d) repeating steps (b) and (c) as desired so as to cause the        production of multiple copies of the newly synthesised nucleic        acid;    -   characterised in that the temperature at which the method is        performed is non-isothermal, and subject to a reduction of at        least 2° C., preferably at least 5° C., during the amplification        process of steps (b)-(d).

In a second aspect, the invention provides apparatus for performing themethod of the first aspect of the invention, the apparatus comprisingtemperature regulation means and programmable control means, theprogrammable control means being programmed to operate the temperatureregulation means to perform a temperature reduction of at least 2° C.,preferably at least 5° C., during the amplification process of areaction mixture used to perform the method of the first aspect.

The amplification process of the method of the invention may be appliedto generally known and conventional amplification techniques includingSDA and NEAR.

Thus, for example, the amplification process may be based on theamplification process employed in strand displacement amplification, orbased on that used in NEAR or indeed any other nucleic acidamplification process which relies on the creation of a single strandednick and subsequent extension from the 3′ end of the nicked strand.Accordingly the teachings of the prior art in relation to theamplification stages of SDA or NEAR will, in general, be equallyapplicable to the amplification process of the method of the presentinvention (other than the teachings of the prior art in relation tomaintenance of constant temperature during the amplification).

Preferably step (a) comprises mixing a sample containing double strandedtarget with two single stranded primers, one of said primers beingcomplementary to a first strand of the target, and the other of saidprimers being complementary to a second strand of the target, such thatthe two primers hybridise to the target and the free 3′ ends of saidprimers face towards one another.

The two primers may conveniently be described as ‘forward’ and ‘reverse’primers.

Desirably both the forward and reverse primers will comprise thesequence of a nicking enzyme recognition site. Typically the nickcreated by a nicking enzyme will be just outside and typically 3′ of thenicking enzyme recognition site.

In a preferred embodiment, the forward primer will comprise a portion ator near its 3′ end which is complementary to, and can hybridise with,the 3′ end of the target sequence antisense strand, whilst the reverseprimer comprises a portion at or near its 3′ end which is complementaryto, and can hybridise with, the 3′ end of the target sequence sensestrand.

In this way, a nicking enzyme recognition site is introduced at oppositeends of the target sequence, and amplification of the target sequence(together with any intervening sequence of the primers downstream of thenick site) is accomplished by performing multiple cycles of polymeraseextension of the forward and reverse primers so as to form a doublestranded nick site, and by nicking of the nick sites with a nickingenzyme, allowing further extension of the nicked primers by a polymeraseetc., essentially as disclosed in, for example, US 2009/0017453, thecontent of which is herein incorporated by reference.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to, inter alia, a method for theamplification of a selected target nucleic acid.

The target may be single stranded, double stranded, or comprise amixture of the two. The target may comprise RNA, DNA or a mixture of thetwo. In particular the target might incorporate one or more modifiednucleotide triphosphates (i.e. a nucleotide triphosphate not normallyfound in naturally occurring nucleic acids), although this is notessential and indeed not preferred.

The target may be selected from the following non-exhaustive list:genomic nucleic acid (which term encompasses the genomic nucleic acid ofany animal, plant, fungus, bacterium or virus), plasmid DNA,mitochondrial DNA, cDNA, mRNA, rRNA, tRNA, or a syntheticoligonucleotide or other nucleic acid molecule.

In particular, the method may additionally comprise an initial reversetranscription step. For example, RNA (e.g. viral genomic RNA, orcellular mRNA, or RNA from some other source) may be used to synthesiseDNA or cDNA using a reverse transcriptase by methods well-known to thoseskilled in the art. The DNA may then be used as a target sequence in themethod of the invention. The original RNA will typically be degraded bythe ribonuclease activity of reverse transcriptase, but if desiredadditional RNAse H may be added after reverse transcription has beencompleted. RNA molecules are often present in samples at greater copynumber than corresponding (e.g. genomic) DNA sequences, hence it may beconvenient to make DNA transcripts from the RNA molecule in order toeffectively increase the copy number of the DNA sequence.

The “target sequence” is the sequence of bases in the target nucleicacid, and may refer to the sense and/or antisense strand of a doublestranded target, and also encompasses, unless the context dictatesotherwise, the same base sequence as reproduced or replicated inamplified copies, extension products or amplification products of theinitial target nucleic acid.

The target sequence may be present in any kind of sample e.g. biologicalor environmental (water, air etc.). A biological sample may be, forexample, a food sample or a clinical sample. Clinical samples mayinclude the following: urine, saliva, blood, serum, plasma, mucus,sputum, lachrymal fluid or faeces.

The sample may or may not be subject to processing before beingcontacted with the primers. Such processing may include one or more of:filtration, concentration, partial-purification, sonication, lysis andthe like. Such processes are well-known to those skilled in the art.

The method of the present invention involves the use of a nick site andmeans for creating a nick at the nick site. A “nick” is the cleavage ofthe phosphodiester backbone of just one strand of a fully, or at leastpartially, double stranded nucleic acid molecule. The nick site is thelocation in the molecule where a nick is made.

In preferred embodiments a “nicking recognition site” will be presentat, within, or near to a nick site. (“Near to” in this context meansthat the nearest base of the nicking recognition site is within 10 basesof the nick site, preferably within 5 bases of the nick site).

The nicking recognition site may comprise at least one strand of therecognition site of a restriction endonuclease, and the nick site maycomprise at least one strand of a nucleic acid base sequence which, whenpresent as a double stranded molecule, is cut by a restrictionendonuclease. Typically a restriction endonuclease will cut both strandsof a double stranded nucleic acid molecule. In the present invention, adouble stranded break can be avoided by the incorporation of one or moremodified bases at or near to the nick site, which modified bases rendera strand of nucleic acid not susceptible to cleavage by the restrictionendonuclease. In this way a restriction endonuclease, which usually cutsboth strands of a double stranded nucleic acid molecule, can be used tointroduce a single stranded nick into a double stranded molecule.Modified bases and the like suitable for achieving this are well-knownto those skilled in the art and include, for example, all alphaphosphate modified nucleoside triphosphates and alpha borano modifiednucleoside triphosphates, specifically; 2′-deoxyadenosine5′-O-(thiotriphosphate), 5-methyldeoxycytidine 5′-triphosphate,2′-deoxyuridine 5′ triphosphate, 7-deaza-2′ deoxyguanosine5′-triphosphate, 2′ deoxyguanosine-5′-O-(1-boranotriphosphate) andothers. Triphosphates including the modified base may be present withina reaction mixture used to perform the amplification process, so thatmodified bases are incorporated at relevant positions during subsequentrounds of amplification to prevent the formation of a site cleavable bythe endonuclease.

In preferred embodiments however the nick is made at the nick site bymeans of a nicking enzyme. These are enzymes which, under normalcircumstances, make only a single stranded break in a double strandednucleic acid molecule. The nicking enzyme has a nicking recognition siteand the nick site may be within the nicking recognition site or may beeither 5′ or 3′ of the recognition site. Many nicking enzymes are knownto those skilled in the art and are commercially available. Anon-exhaustive list of examples of nicking enzymes includes: Nb.Bsml,Nb.Bts, Nt.Alwl, Nt.BbvC, Nt.BstNBI, and Nt.Bpu101. The latter enzyme iscommercially available from ThermoFisher Scientific; the others areavailable from e.g. New England Biolabs.

In preferred embodiments, the nicking enzyme is introduced into thereaction mixture at the outset of the method (e.g. within one minute ofcontacting the sample with primers and DNA polymerase). However, in someinstances it may be desirable to introduce the nicking enzyme into thereaction mixture after a longer delay (e.g. to allow the temperature tofall closer to the optimum temperature of the nicking enzyme).

The method of the invention involves the use of a DNA polymerase.Preferably the method of the invention comprises the use of at least onethermophilic

DNA polymerase (i.e. having an optimum temperature in excess of 60° C.).Preferably the DNA polymerase is a strand displacing polymerase.Preferably the DNA polymerase has no exonuclease activity. Preferablythe DNA polymerase is a strand displacing polymerase with no exonucleaseactivity, and is also preferably thermophilic.

Examples of preferred DNA polymerases include Bst polymerase, Vent® DNApolymerase, 9° N polymerase, Manta 1.0 polymerase (Qiagen), BstXpolymerase (Qiagen), and Bsm DNA polymerase, large fragment(ThermoFisher Scientific).

In some embodiments, the method of the invention may convenientlycomprise a pre-amplification or enrichment step. This is a step in whichthe target sequence is contacted with forward and reverse primers andDNA polymerase, but no nicking enzyme. This typically lasts for about2-5 minutes and produces an initial (linear) amplification of the targetsequence of about 1,000 fold, which can be especially useful if thetarget sequence is present in the sample at low copy number.

In some embodiments, the pre-amplification or enrichment step isperformed using a mesophilic DNA polymerase such as Exo-Minus Kienow DNAPolymerase or Exo-Minus psychrophile DNA polymerase from Cenarchaeumsymbiosum, at a temperature below 50° C., and the mixture issubsequently heated above 50° C. to denature or inactivate thethermolabile DNA polymerase, and then a thermophilic DNA polymerase isadded for downstream amplification.

Typically, the method of the invention comprises a detection step, inwhich one or more of the direct or indirect products of theamplification process is detected and optionally quantified, thisindicating the presence and/or amount of the target in the sample. Thereare a great many suitable detection and/or quantification techniquesknown, including: gel electrophoresis, mass spectrometry, lateral flowcapture, incorporation of labelled nucleotides, intercalating dyes,molecular beacons and other probes, especially specifically hybridisingoligonucleotides or other nucleic acid containing molecules.

The product or products which are detected in the detection step may bereferred to herein as the “detection target”. The ‘target’ in relationto the detection step, is not necessarily the same as the ‘target’ inthe amplification process and indeed the two molecules will usually bedifferent to at least some extent, although they may have some sequence(typically 10-20 bases) in common, where the detection target comprisesa nucleic acid molecule or oligonucleotide.

Nucleic acid detection methods may employ the use of dyes that allow forthe specific detection of double-stranded DNA Intercalating dyes thatexhibit enhanced fluorescence upon binding to DNA or RNA are well known.Dyes may be, for example, DNA or RNA intercalating fluorophores and mayinclude inter alia the following: acridine orange, ethidium bromide,Pico Green, propidium iodide, SYBR I, SYBR II, SYBR Gold, TOTO-3 (athiaxole orange dimer) Oli Green and YOYO (an oxazole yellow dimer).

Nucleic acid detection methods may also employ the use of labellednucleotides incorporated directly into the detection target sequence orinto probes containing sequences complementary or substantiallycomplementary to the detection target of interest. Suitable labels maybe radioactive and/or fluorescent and can be resolved in any of themanners conventional in the art. Labelled nucleotides, which can bedetected but otherwise function as native nucleotides (e.g. arerecognised by and may act as substrates for, natural enzymes), are to bedistinguished from modified nucleotides, which do not function as nativenucleotides.

The presence and/or amount of target nucleic acids and nucleic acidsequences may be detected and monitored using molecular beacons.Molecular beacons are hair-pin shaped oligonucleotides containing afluorophore at one end and a quenching dye (“quencher”) at the oppositeend. The loop of the hair-pin contains a probe sequence that iscomplementary or substantially complementary to a detection targetsequence and the stem is formed by the annealing of self-complementaryor substantially self-complementary sequences located either side of theprobe sequence.

The fluorophore and the quencher are bound at opposite ends of thebeacon. Under conditions that prevent the molecular beacon fromhybridizing to its target or when the molecular beacon is free insolution, the fluorophore and quencher are proximal to one another,preventing fluorescence. When the molecular beacon encounters adetection target molecule, hybridization occurs; the loop structure isconverted to a stable, more rigid conformation causing separation of thefluorophore and quencher allowing fluorescence to occur (Tyagi et al.1996, Nature Biotechnology 14: 303-308). Due to the specificity of theprobe, the generation of fluorescence is substantially exclusively dueto the presence of the intended amplified product/detection target.

Molecular beacons are highly specific and can distinguish nucleic acidsequences differing by a single base (e.g. single nucleotidepolymorphisms). Molecular beacons can be synthesized with differentcoloured fluorophores and different detection target complementarysequences, enabling several different detection targets in the samereaction to be detected and/or quantified simultaneously, allowing“multiplexing” of a single PoC assay to detect a plurality of differentpathogens or biochemical markers.

For quantitative amplification processes, molecular beacons canspecifically bind to the amplified detection target followingamplification, and because non-hybridized molecular beacons do notfluoresce, it is not necessary to isolate probe-target hybrids toquantitatively determine the amount of amplified product. The resultingsignal is proportional to the amount of the amplified product. This canbe done in real time. As with other real time formats, the specificreaction conditions must be optimized for each primer/probe set toensure accuracy and precision.

The production or presence of detection target nucleic acids and nucleicacid sequences may also be detected and monitored by fluorescenceresonance energy transfer (FRET). FRET is an energy transfer mechanismbetween two fluorophores: a donor and an acceptor molecule. Briefly, adonor fluorophore molecule is excited at a specific excitationwavelength. The subsequent emission from the donor molecule as itreturns to its ground state may transfer excitation energy to theacceptor molecule (through a long range dipole-dipole interaction). FRETis a useful tool to quantify molecular dynamics, for example, in DNA-DNAinteractions as seen with molecular beacons. For monitoring theproduction of a specific product a probe can be labelled with a donormolecule on one end and an acceptor molecule on the other.Probe-detection target hybridization brings a change in the distance ororientation of the donor and acceptor and a change in the FRETproperties is observed. (Joseph R. Lakowicz. “Principles of FluorescentSpectroscopy”, Plenum Publishing Corporation, 2^(nd) edition (Jul. 1,1999)).

The production or presence of detection target nucleic acids may also bedetected and monitored by lateral flow devices. Lateral flow devices arewell known. These devices generally include a solid phase fluidpermeable flow path through which fluid flows by capillary force.Examples include, but are not limited to, dipstick assays and thin layerchromatographic plates with various appropriate coatings. Immobilized inor on the flow path are various binding reagents for the sample, bindingpartners or conjugates involving binding partners for the sample, andsignal producing systems. Detection of analytes can be achieved inseveral different ways including: enzymatic detection, nano-particledetection, colorimetric detection, and fluorescence detection. Enzymaticdetection may involve enzyme-labelled probes that are hybridized tocomplementary or substantially complementary nucleic acid detectiontargets on the surface of the lateral flow device. The resulting complexcan be treated with appropriate markers to develop a readable signal.Nanoparticle detection involves bead technology that may use colloidalgold, latex and paramagnetic nanoparticles. In one example, beads may beconjugated to an anti-biotin antibody. Target sequences may be directlybiotinylated, or target sequences may be hybridized to a sequencespecific biotinylated probes. Gold and latex give rise to colorimetricsignals visible to the naked eye and paramagnetic particles give rise toa non-visual signal when excited in a magnetic field and can beinterpreted by a specialized reader.

Fluorescence-based lateral flow detection methods are also known, forexample, dual fluorescein and biotin-labelled oligo probe methods, orthe use of quantum dots.

Nucleic acids can also be captured on lateral flow devices. Means ofcapture may include antibody dependent and antibody independent methods.Antibody-independent capture generally uses non-covalent interactionsbetween two binding partners, for example, the high affinity andirreversible linkage between a biotinylated probe and a streptavidincapture molecule. Capture probes may be immobilized directly on lateralflow membranes.

The entire method of the invention, or at least the amplificationprocess portion of the method, may be performed in a reaction vessel(such as a conventional laboratory plastics reagent tube e.g. fromEppendorf®) or may be performed in and/or on a solid support. The solidsupport may be porous or non-porous. In a particular embodiment thesolid support may comprise a porous membrane material (such asnitrocellulose or the like). More especially the solid support maycomprise or form part of a porous lateral flow assay device, asdescribed above. Alternatively, the solid support may comprise or formpart of a microfluidics-type assay, in which one or more solidnarrow-bore capillary tubes are used to transport a liquid along anassay device.

In preferred embodiments, all or at least part of the method of theinvention may be performed using a point-of-care (PoC) assay device. APoC device typically has the following characteristics: it is cheap tomanufacture, is disposed of after a single use, is generallyself-contained not requiring any other apparatus or equipment to performor interpret the assay and, desirably, requires no clinical knowledge ortraining to use.

Examples of primers suitable for use in the invention are disclosedherein. Other examples which may be suitable for use in the method ofthe invention are disclosed in, inter alia, US 2009/0017453 and EP2,181,196, the content of both of which is incorporated herein byreference. The person skilled in the art will be readily able to designother primers suitable for the amplification of other target sequenceswithout undue experimentation.

As explained elsewhere, primers of use in the invention will preferablycomprise not only a target complementary portion, but also a nickingendonuclease binding site and nicking site, and a stabilizing portion.Preferred primers may contain self-complementary sequence which can forma stem-loop structure in the primer molecule.

Primers of use in the method of the invention may comprise modifiednucleotides (i.e. nucleotides not found in naturally occurring nucleicacid molecules). Such modified nucleotides may conveniently be presentin the target complementary portion of the primer, and/or elsewhere inthe primer. Preferred examples of modified nucleotides are 2′-modifiednucleotides, especially 2′ O-methyl modified nucleotides, although manyother modified nucleotides are known to those skilled in the art.

Temperature Profile

The method of the present invention, whilst not isothermal, does notrequire thermal cycling. As a result the method of the invention doesnot require the use of the relatively complex thermal cycling apparatusused in PCR, and accordingly lends itself more readily to application ina PoC context.

“Thermal Cycling” or temperature cycling means that, in particular, thetemperature of a reaction mixture is held at a particular temperature(say ti) for a particular length of time (typically at least 30seconds). The temperature is then adjusted (either up or down) beforebeing returned to the previously maintained temperature.

Typically non-isothermal nucleic acid amplification reactions, such asPCR, require the performance of multiple thermal steps per cycle (i.e.at least two or more), and multiple thermal cycles per reaction.

The temperature reduction in the method of the present invention isdeliberate, and controlled, in the sense that the magnitude of thetemperature reduction is above a predetermined minimum level and below apredetermined maximum level. In addition, the rate of temperaturedecrease is preferably within a predetermined range.

The initial step (a) in the method of the invention involves contactinga target sequence with a primer having at least a portion which iscomplementary to the target sequence, in conditions which permit theprimer to hybridise to the target, at least temporarily. This may bedescribed as the “initiation” phase.

This step is typically accomplished at a temperature in the range 50-65°C., preferably in the range 52-62° C., more preferably in the range54-62° C., most preferably in the range 58-62° C. The reaction mixturecomprising the target and the primer may be held at this temperature fora suitable period of time. The optimum temperature, and the optimumperiod of time for which the reaction mixture is held at thistemperature, may be determined by the person skilled in the art giventhe benefit of the present disclosure, and these may be affected byparameters such as the length of the target sequence, the length of theprimers—and especially the length of the portion of the primer which iscomplementary to the target, the G:C content of the target: primerhybrid, the pH and salt concentration of the reaction mixture. A typicalinitial temperature holding time might be in the range 5 seconds to 5minutes, preferably 10 seconds to 3 minutes. Typical conditions topermit the initial hybridisation event in step (a) will be known tothose skilled in the art and are described in the accompanying examples.

The temperature range of 58-62° C. is preferred for the initiationphase. This is thought to be sufficiently high to minimise the formationof primer dimers (and hence to reduce the amount of non-specificamplification), and increase the probability of creating potential“initiation sites” in the target duplex, whilst being low enough toallow at least some of the primer molecules to hybridise to the target.

The subsequent reduction in temperature helps stabilise thehybridisation of the relatively short primers and the extensionproducts, rather than hybridisation of the primers to the originaltarget molecule. It is further hypothesized that additional cooling ofthe reaction mixture facilitates hybridisation of the detection probe tothe detection target.

During the amplification process set out in steps (b)-(d) of the method,the temperature of the reaction mixture is reduced. This may be done ina regulated manner, for example, using a temperature regulation means toreduce the temperature of the reaction mix according to a predeterminedtemperature profile. The temperature reduction may commence immediatelyafter the initiation phase (step a). Advantageously the volume of thereaction mix is small, so that the thermal capacity of the reaction mix(and the reaction vessel or substrate in or on which the reaction isperformed) is reduced.

Conveniently the reaction mix has a volume of less than 100 μl,preferably less than 50 μl, more preferably less than 25 μl and mostpreferably less than 20 μl. In this way, the temperature of the reactionmix can be more accurately and more swiftly regulated by the temperatureregulation means. In suitable embodiments the temperature regulationmeans may be very simple (e.g. a fan) or may be dispensed with entirely,with sufficient cooling being largely or wholly achieved by passivemeans (e.g. by thermal radiation from the reaction mixture). Typicallythe reaction mix volume may be in the range 1-50 μl, preferably 1-20 μland more preferably 1-10 μl.

The reaction mix volume may be less than 10 μl. In particular, themethod of the invention may employ a “digital PCR”-type approach (seereview by Morley 2014 Biomolecular Detection and Quantification 1, 1-2)in which the sample is diluted and split into many (usually severalhundred, a few thousand, or even million) aliquots which are processedin parallel: some of the aliquots will contain a target sequence andsome will not: if no target sequence is present no signal is generated.The proportion of negative aliquots can be used to deduce the numberand/or concentration of the target sequence in the original sample. Insuch embodiments, the reaction mix volume in each aliquot may be verysmall, typically however the minimum volume would be 2500 nl, preferablyat least 50 μl.

The temperature may be reduced in any desired profile. For instance, thetemperature may be reduced according to a substantially linear profile(i.e. with an essentially constant rate of temperature reduction), ormay be reduced in any non-linear manner, including a curve or astep-wise fashion, or any combination of linear and non-linear profiles(e.g. one or more periods of constant rate temperature reduction, whichrate may be zero or relatively low, alternating with periods ofrelatively high rates of temperature reduction).

The temperature profile of the reaction in accordance with the inventionis such that the temperature of the reaction is not allowed to return tothe temperature at which the “initiation” phase is performed. Thus inthe method of the present invention there is no oscillation about apredetermined temperature and no “return” to a predetermined temperaturecontrary to, for example, the disclosure of WO 2011/030145.

The temperature of the reaction mix at the start of the amplificationprocess will typically be the same as that in step (a) e.g. preferablyin the range 54-62° C. and most preferably 58-62° C. During theamplification process, the temperature falls by at least 2° C.,preferably by at least 3, 4 or 5° C., more preferably by at least 8, 9or 10° C., and most preferably by at least 13, 14 or 15° C., although itwill be appreciated that the preferred magnitude of the temperaturedrop, in absolute terms, may be at least partially dependent on theselected initial temperature at the start of the amplification process,wherein a lower initial temperature (e.g. in the range 45-55° C.) mightpredicate a lower temperature drop and/or a lower rate of temperaturereduction.

Typically the maximum magnitude of the temperature decrease during theamplification process is about 20° C., although it will be appreciatedthat the maximum temperature decrease might be less than this (e.g. 16,17, 18 or 19° C.) or more (e.g. 25 or 30° C.).

In preferred embodiments the magnitude of the temperature reduction ofthe reaction mix during the amplification process may be in the range5-40° C., preferably in the range 8-35° C., more preferably in the range8-30° C. or even 8-25° C., and most preferably in the range 8-20° C. Thetypical initial temperature of the reaction mixture at the start of theamplification process is in the range 50-62° C., preferably 54-62° C.,more preferably in the range 56-60° C., and most preferably in the range58-60° C.

In preferred embodiments, the temperature reduction during theamplification process (steps (b)-(d) of the method of the invention)includes a reduction encompassing the range 54 to 50° C., 56 to 50 or 58to 50, more preferably 58 to 45, 58 to 40 or even 60 to 40° C. It willbe understood that the temperature reduction during the amplificationprocess may be greater than the stated ranges defined above. That is,the maximum temperature may exceed the upper temperature of the statedrange and/or the minimum temperature may be beneath the lowertemperature of the stated range.

The end temperature of the amplification reaction is preferably selectedfor compatibility with the chosen detection method. For example, if thedetection method involves the use of an enzyme label, it may bedesirable to arrange the end temperature of the amplification reactionto be compatible with the enzyme and, for example, within ±5° C. of theoptimum temperature of the enzyme. Alternatively, where the detectionmethod involves the use of a hybridising detection probe, such as amolecular beacon or the like, it will be advantageous to arrange the endtemperature of the amplification reaction to be selected so as to becompatible with the Tm of the detection probe/detection target duplex.

For example, the end temperature may conveniently be below the Tm of thedetection probe/detection target duplex, preferably at least 2° C.below, so as to facilitate the hybridisation of the probe to thedetection target.

The typical average rate of temperature reduction during theamplification process is in the range −0.10 to −6.0° C. min⁻¹,preferably in the range −0.20 to −3.5° C. min⁻¹ more preferably in therange −0.30 to −3.5° C. min⁻¹, and most preferably in the range −0.40 to−3.5° C. mind. As will be apparent from the foregoing, the actual rateof temperature reduction at any one instant during the amplificationprocess might deviate from the preferred average rate, depending on thenature of the temperature reduction gradient.

In some embodiments the temperature reduction gradient is substantiallylinear for at least 3 minutes, more preferably at least 4 minutes andmost preferably over most of the duration of the amplification process.Typically the temperature reduction gradient is substantially linearover a period in the range 3-12 minutes, preferably in the range 4-10minutes, more preferably in the range 4-8 minutes. For present purposes“substantially linear” means that, for any second order polynomialdescribing the temperature gradient, the magnitude of the coefficient ofX is less than 5% of the value of the coefficient of Y.

A large number of different techniques can be envisaged for achievingthe desired temperature reduction during the amplification process.These may include one or both of the following: (a) ceasing to applyheat to the reaction mix and/or removing the reaction mix from a heatedand/or insulated environment and allowing the reaction mix to coolessentially by passive heat-loss to the ambient environment; (b)application of active cooling to the reaction mix. Active cooling mayinvolve exposing the reaction mix to a cooled environment e.g. placingthe reaction mix in thermally communicating (conducting, radiating orconvection) contact with a cooled medium, especially a fluid. This couldcomprise, for example, contacting the reaction mix with a chilled waterbath, using a fan to blow cold air or other gas over or through thereaction mix, contacting the reaction mix with a reaction mix-compatiblecoolant, which may be a gas, liquid or solid, or the use of aPeltier-type cooling device. For example, the reaction mix-compatiblecoolant may be a reaction mix compatible buffer in frozen or chilledliquid form. The addition of a cold buffer would tend to dilute thereaction mix, so if this approach is adopted it may be preferred to usesmall volumes (e.g. less than 1-2 μl) of coolant at a temperature wellbelow (i.e. more than 20° C. cooler than) the temperature of thereaction mix.

Any active cooling steps may be applied discontinuously during theamplification process so as to achieve a desired temperature reductionlevel and/or a desired temperature reduction profile. In particular,active cooling may be performed at two or more interspersed intervalsduring the amplification process, and may optionally be combined withpassive cooling, simultaneously or alternating.

In general, it is preferred to achieve the desired amount and rate oftemperature reduction substantially by purely passive means, since thissimplifies the method and any apparatus or kit required for performingthe method. In order to achieve the desired amount and rate of coolingby substantially purely passive means, it is desirable that the volumeof the reaction mix is small, so as to reduce its thermal capacity, asnoted previously.

It is a preferred feature of the method of the invention that theamplification process may utilise a first polymerase having an optimumtemperature, and a second polymerase having an optimum temperature,wherein the optimum temperature of the second polymerase is lower thanthe optimum temperature of the first polymerase. Accordingly, the firstpolymerase may be especially active near the start of the amplificationprocess, since the temperature of the reaction mix may be at or close tothe optimum temperature of the first polymerase.

Thus, for example, the first polymerase may advantageously be a“thermophilic” enzyme (i.e. having an optimum temperature in excess of60° C.).

Conversely, the second polymerase has a lower optimum temperature thanthe first polymerase. As the amplification process continues, thetemperature of the reaction mix falls and approaches closer to theoptimum temperature of the second polymerase. Thus the second polymerasebecomes increasingly active, which at least partially compensates for adeclining rate of reaction, which decline is due to (i) a generalthermodynamic slowing of the reaction due to the lower temperature and(ii) the temperature of the reaction mix possibly falling below theoptimum temperature of the first polymerase, resulting in reducedcatalysis.

Advantageously the optimum temperature of the second polymerase is inthe range 30-55° C., more preferably in the range 30-45° C.

In a particular embodiment the second polymerase may be Klenow fragmentof DNA polymerase I or Bsu polymerase.

It is conceivable that even a third or further polymerase, preferablywith a yet lower, third optimum temperature, may be used.

The second polymerase is preferably in the reaction mix from the outsetof the amplification process but, if desired, the second polymerasecould be added after a delay, allowing the temperature of the reactionmix to be reduced from a high initial temperature. This may beadvantageous it: for example, the second polymerase is especiallythermolabile and likely to be substantially denatured if present at therelatively high temperatures normally employed at the start of theamplification process.

In a manner exactly analogous to the foregoing, the amplificationprocess may utilise first and second nicking enzymes with, respectively,higher and lower optimum temperatures. The first and second nickingenzymes may be used in conjunction with a single polymerase or multiplepolymerases as the case may be.

As above, the use of a second nicking enzyme with a lower optimumtemperature may at least partially offset the reduced rates of reactionexpected as the temperature falls during the amplification process.

Thus, in some embodiments, the temperature of the reaction mix may startat, or may be reduced during the course of the amplification process to,a temperature below the optimum temperature of the first polymeraseand/or the first nicking enzyme and will tend to approach, and may evenreach, the optimum temperature of the second polymerase and/or secondnicking enzyme.

Conveniently, in some embodiments, the method of the invention maycomprise the step of contacting the reaction mixture with a degradativeenzyme which degrades nucleic acid. Desirably this step is not effecteduntil a user has obtained the desired outcome of the amplificationreaction (e.g. detection of a pathogen). Typically therefore thedegradative enzyme is added to the reaction mixture after theamplification process has reached a desired end-point. Preferably thedegradative enzyme is thermolabile so that, in the event that it isinadvertently introduced into or contacted with reaction mix before theamplification process has attained the desired end-point, thetemperature is sufficient to substantially denature or otherwiseinactivate the enzyme. Suitable examples include cod uracil-DNAglycosylase (“UDG”) available from ArcticZymes® and Antarcticthermolabile UDG (available from New England BioLabs). These enzymes arerapidly and irreversibly inactivated upon exposure to a temperature of55° C. or 50° C. respectively, and the term “thermolabile” in relationto the degradative enzyme, should be construed accordingly.Alternatively, a thermally-sensitive degradative enzyme could be used(i.e. one which is at least partially active below 50° C. but,reversibly, substantially inactive above 55° C.).

The invention will now be further described by way of illustrativeexample and with reference to the accompanying drawings, in which:

FIGS. 1A-1C are schematic representations of a typical embodiment of aprimer useful in performing the method of the invention;

FIGS. 2A and 2B are schematic representations of the initiation phaseand exponential amplification phase respectively of a nucleic acidamplification reaction suitable for performing the method of theinvention;

comprising

FIGS. 3 to 11 are graphs of (background subtracted) fluorescence(arbitrary units) and temperature (° C.) against time (minutes);

FIGS. 12A-12C are graphs of (background subtracted) fluorescence(arbitrary units) against time for individual replicates ofamplification reactions;

FIG. 13 is a scatter chart comparing the time taken to achieveamplification from 10 copies of template sequence under “STAR”conditions in accordance with the invention or under isothermalconditions;

FIGS. 14A and 14B are graphs of (background subtracted) fluorescence(arbitrary units) and temperature (° C.) against time using isothermalamplification conditions (63° C. or 49° C. respectively);

FIGS. 15A, 15B and 15C are graphs of (background subtracted)fluorescence (arbitrary units) and temperature (° C.) against time(minutes) for individual replicates (10 copies or 100 copies; broken andsolid lines respectively) for amplification reactions in accordance withthe invention under various temperature profiles;

FIGS. 16A and 16B are graphs of (background subtracted) fluorescence(arbitrary units) and temperature against time (minutes) foramplification reactions in accordance with the invention under differenttemperature profiles;

FIGS. 17A and 17B are graphs of (background subtracted) fluorescence(arbitrary units) and temperature (° C.) against time (minutes) foramplification reactions in accordance with the invention performed usingprimers containing 6 (FIG. 17A) or 7 (FIG. 17B) O-methylated bases; and

FIG. 18 is a graph of (background subtracted) fluorescence (arbitraryunits) against time (minutes) for amplification reactions performed inaccordance with the invention using a DNA target generated by reversetranscription of Listeria monocytogenes 23S RNA.

EXAMPLES Example 1: Protocols for Testing Temperature Decreases

The effect of temperature decrease on an amplification reaction wastested by comparing amplifications using temperature decreases over timevs standard isothermal conditions. The decreasing temperatureamplification is referred to herein as “STAR” (Selective TemperatureAmplification Reaction). These comparisons were carried out using aprotocol as described below unless noted.

Enzymes, Oligonucleotides, and Target

Chlamydia trachomatis (Ct) was used as the initial target for thedevelopment of the STAR mechanism. Chlamydia trachomatis Serovar J (ATCCVR-886) genomic DNA was acquired from American Type Culture Collection(Manassas, VA). The open reading frame 6 region of the cryptic plasmidwas amplified with primers STARctF6la (SEQ ID NO: 1,5′-CGACTCCATATGGAGTCGATTTCCCCGAATTA-3′) and STARctR6lc (SEQ ID NO: 2,5′-GGACTCCACACGGAGTCTTTTTCCTTGTTTAC-3′). The resulting DNA template wasdetected using a molecular beacon STARctMBI (SEQ ID NO:3,5′-FAM/ccattCCTTGTTTACTCGTATTTTTAGGaatgg/BHQ1-3′) as described in EP No.0728218. Manta 1.0 DNA polymerase was purchased from Enzymatics(Beverly, MA). Nt.BstNBI nicking endonuclease was purchased from NewEngland BioLabs (Ipswich, MA) described in U.S. Pat. No. 6,191,267.

Oligonucleotides and molecular beacons were synthesized by IntegratedDNA Technologies (Coralville, IA.) and Bio-Synthesis (Lewisville, TX).The general features of the primers used in the STAR reactions were asfollows:

Primer sets were constructed with a stabilizing region 5′ of the nicksite and a target specific binding region 3′ of the nick site (FIG. 1A).Primers were constructed in such a way that a stem and loop structurecan form at the 5′ end of the oligonucleotide by creating aself-complementary structure that forms at least part of the stem. TheTm of this structure was chosen to direct either linear or exponentialamplification dependent upon the temperature of the reaction at a giventime. The stem further encompassed at least a portion of the nickingenzyme recognition sequence. The nicking enzyme recognition sequence inthe primers is part of the double stranded stem structure, but at leastone nucleotide is single stranded to prevent nicking. If desired, thesequence that is complementary to the target sequence may comprise asecondary structure or may be free of secondary structure. Further, thissequence may contain modified nucleotides such as 2′ modifications orphosphorothioate bonds.

Referring to FIG. 1A, the “primer region” is the sequence that iscomplementary to, and anneals to, the target sequence. The “NEB region”is the nicking endonuclease binding region i.e. the recognition regionof the nicking enzyme which, in this instance, nicks the primer at asite four nucleotides downstream of the end of the NEB region The“Amplification loop” provides primer stabilization and hybridization forthe amplification process and is looped on itself viaself-complementarity during the initiation phase to reduce backgroundnon-specific amplification. FIGS. 1B and 1C show slightly differentembodiments of primers useful in the method of the invention. The primerstructure is essentially identical to the embodiment shown in FIG. 1A,but the altered primers include modified bases in the “primer region”.Specifically at the 3′ end of the primer region there Is a string ofconsecutive 2′ O-methylated bases. In FIG. 1B this string is 7 baseslong and in FIG. 1C the string is 6 bases long. Primers of the sortshown in FIGS. 1B and 1C were used in Example 8 below.

The summary of the oligonucleotides and amplification mechanism found ina reaction comprises (1) a target nucleic acid molecule; (2) two or moreprimer oligonucleotide molecules comprising some number ofoligonucleotides that are complementary to the target nucleic acidmolecule and (3) a site within the primer that can be nicked by anicking enzyme The method involves contacting a target nucleic acidmolecule with a polymerase, two or more printer oligonucleotides, eachof which specifically binds to a complementary sequence on the targetnucleotide molecule, and a nicking enzyme; and, under non-isothermalconditions, generating a detectable amplicon that comprises at least aportion of a primer oligonucleotide that binds a target sequence. Theoverall STAR reaction can be understood to undergo two distinct phases;initiation and exponential amplification. The initiation phase is theinitial formation of an exponential—template duplex from whichexponential amplification can occur. These two phases are illustratedschematically in FIGS. 2A and 2B. In those figures, the triangle symbolrepresents the nicking enzyme and the hexagon symbol represents the DNApolymerase. Initial contact of the primer to a target nucleic acidoccurs followed by extension and generation of a forward initiationtemplate. Then the opposite strand primer binds to the newly generatedforward initiation template, extending in the direction toward, andthrough, the initiation template's nick site. This initial process canbe understood to involve the polymerase for extension and is highlyprone to primer dimer-formation and false amplification of truncated orbackground products. Once nicking begins on either strand the polymerasewill infiltrate the nick site and extend toward the opposite primer andthrough the nick site.

Once this cycle of nicking followed by polymerase extension has occurredon both the forward initiation strand and reverse initiation strand, aduplex is formed known as an exponential duplex. The second phase of thereaction begins; this exponential process of amplification feeds intoitself as each new template generated from a nick and extension is now atarget for another primer.

It is now understood that the second phase requires an active nickingendonuclease for fast template generation. It was previously known thatthis nick strand displacement replication occluded the need fortemperature cycling thus the reaction could, and has always been,performed at constant temperature. The present novel discovery allowsfor unique and distinct amplification methods with significantly greaterperformance than existing methods, including high yield of product withgreat specificity in a short time period.

Amplification Conditions

The basic Selective Temperature Amplification Reaction (STAR) mixturecontains two primers, polymerase and nicking enzyme (referenced above).The reactions were performed in a final volume of 20 μl, including 0.41μM of the forward primer, 0.2 μM of the reverse primer, 0.18 μMmolecular beacon, 10 μl STAR Master Mix and 5 μl DNA sample. STAR mastermix contains the following reagents; 15 mM MgSO₄, 90 mM Tris-HCl (pH8.5), 300 μM each dNTPs, 15 mM (NH₄)₂SO₄, 15 mM Na₂SO₄, 1 MM DTT, 0.01%Triton X-100, 7U nicking endonuclease, 48U polymerase. The temperatureof the reactions was isothermal or varied based upon the amount oftemperature reduction. If the temperature during amplification in eachreaction starts at 60° C. and decreases a specified amount every 15seconds or 1 minute, then for example a negative 0.5° C. rate (i.e. a0.5° C. decrease in temperature every 15 seconds) for 10 minutes wouldresult in a temperature reduction from 60° C. to 40° C. over the courseof the reaction. Amplification and STAR product detection were performedwith the Agilent Mx:3005 P QPCR apparatus (Agilent). The following tablelists the temperature profiles tested, except where noted:

TABLE 1 pre-reaction incubation Start Temperature Decrease FinishIsothermal Conditions 60° C. 60° C. none 60° C. 56° C. 56° C. none 56°C. 50° C. 50° C. none 50° C. STAR Conditions 60° C. 60° C. −0.1° C. per15 seconds 56° C. 60° C. 60° C.   0.2° C. per 15 seconds 52° C. 60° C.60° C. −0.5° C. per 15 seconds 40° C. 60° C. 60° C. −0.8° C. per 15seconds 32° C. 60° C. 60° C. −1.0° C. per 15 seconds 20° C. 60° C. 60°C. −1.0° C. per minute 51° C.

The pre-reaction incubation is to allow the reagents to come totemperature to test the effect of decreasing temperatures onamplification kinetics, enzyme performance, and signal fluorescence.Running reactions in this manner removes increasing temperaturevariables and allows for a direct comparison between existing isothermalamplification techniques and the novel STAR method.

Amplification Procedure

The exact steps under which an amplification reaction was performed areas follows: 1) prepare master mix; 2) prepare primers with target or notarget; 3) add primer mixes to row A-G of a 96 well plate dependent onnumber of reactions to be done per plate; 4) add master mix to row H ofthe same 96 well plate; 5) seal plate and do a pre-reaction incubationfor 2 minutes; 6) transfer master mix from row H to each primer mix row,waiting 15 seconds between transfers; 7) seal and initiate preselectedtemperature profile and data collection.

During the course of a reaction amplified product was measured every 15seconds by using the molecular beacon as described above. Thefluorescence of the molecular beacon in the reaction mixture wasmonitored to measure the amount of specific product being generatedduring a reaction. Specific product generated during a reaction binds tothe molecular beacon separating the fluorophore from the quencher,generating fluorescence. Fluorescence measurements were backgroundsubtracted based upon the average of the first 3 readings of eachreaction well, before amplification begins. Further characterization wasdone based upon a rise from baseline threshold level (TL). The TL waschosen close to the baseline of the background subtracted fluorescencebut above the range of random fluctuations. The decrease in temperaturecauses molecular beacon baseline fluorescence to decrease due toincreased stem strength, causing a constant linear baseline decrease asthe quencher and fluorophore have greater interaction. The TL of 2000was chosen for all reactions. For comparison an exact number wasdetermined based on time to amplification to reach the TL, referred toas the A_(T) value. Using the A_(T) value allows for comparisons fromone plate to another.

Example 2: Results Using Unmodified Primers

To demonstrate the improvement that STAR provides over currentisothermal technologies, amplifications were carried out using 18replicates for target and 6 replicates for no target. The STAR reactionsshow a dramatic improvement in speed, sensitivity, and totalfluorescence in comparison to isothermal conditions. In particular, therange of −0.8° C. minute to −3.2C° minute was markedly better than allisothermal conditions (FIGS. 3 to 11 ). It is surprising and unexpectedthat such a significant drop in temperature still generates excellentresults. Without limiting the Applicant to any particular theory, it isbelieved that the amplification improvements can be attributed to atleast three characteristics, discussed further below.

The results of experiments using unmodified primers are shown in FIGS.3-11 . In those figures, the temperature profile is indicated by thebackground shading. The amount of signal (fluorescence) for the“non-target” negative controls is indicated by the dark plot. The amountof signal generated in the presence of 10 or 100 copies of target(genomic DNA of C. trachomatis) is indicated by the lighter plots.

FIGS. 3, 4 and 5 show the results for isothermal amplifications (i.e.not according to the method of the invention) at 50, 56 and 60° C.respectively. As can be seen in FIG. 3 , there was essentially nospecific amplification at 50° C., strong amplifications at 56° C. (FIG.4 ), at least for 100 target copy number, and low amplification at 60°C. (FIG. 5 ).

FIGS. 6-10 show the results obtained for non-isothermal (STAR)amplification reactions in accordance with the invention, in which thetemperature was reduced during the amplification. The rate oftemperature reduction was linear, ranging from −0.1° C. per 15 seconds(i.e. −0.4° C. per minute) in FIGS. 6 , to −1.0° C. per 15 seconds (i.e.−4.0° C. per minute) in FIG. 10 . It can be seen that, in all instances,the reactions with 100 copies of target generated more fluorescencesignal than the reactions with 10 copies of target, as would beexpected. More significantly, the reactions produced much more signalthan the equivalent isothermal amplifications, especially for the 10target copy number reactions. In addition, detectable signal wasproduced more quickly than in the equivalent isothermal reactions.

Similar results were obtained when the method of the invention wasperformed using a non-linear, stepwise temperature reduction (as shownin FIG. 11 ).

The inventors also found (data omitted for brevity) that the variationin amount of signal between different replicates in STAR reactions wasfar lower than that between replicates in isothermal reactions, provingthat the method of the invention generated much more consistent results.The following comments offer a possible mechanism by which the method ofthe invention might confer the advantages noted above.

In most nucleic acid amplification reactions primer dimers eventuallyform, competing for limited reagents and at low target concentrationsprimer dimers may become the primary amplification pathway for areaction. Limiting or delaying the formation of primer dimers, even by asmall amount, provides significant benefits to a reaction. Because ofthe rapid nature of the amplification reaction, delaying primer dimerformation allows for preferred amplification pathways to be favoured(i.e. template generation) improving all aspects of amplification. Byinitiating reactions at elevated temperatures these template pathwaysbecome favoured and even preferred. This is seen by the improvedsensitivity in the STAR method, improved fluorescence signal, tightergrouping of replicates (i.e. greater reproducibility) and increasedspeed.

After the initiation phase of the reaction the exponential phase begins.Since the template pathway has been favoured over errant pathways it isdesirable to generate as much product as quickly as possible, and thisis facilitated by STAR. One of the most likely limiting steps to thisgeneration is the nicking of the sites by the nicking endonuclease. Asthe temperature of the reaction mix is reduced, it approaches the mostfavourable temperature for the nicking endonuclease, and the reactionefficiency is increased, generating as much template as possible fordetection.

As the temperature decreases further molecular beacons favour templatedetection and decreased fluorescence background. The melting temperatureof the templates to the molecular beacons becomes significantly higherthan the detection temperature, generating improved signal as lesstemplates melt from the molecular beacon. Furthermore, due to thedecreased temperature, stem melting temperatures become higher thanreaction temperatures. Thus the molecular beacon favours a closed phasewhen no template is present, generating less background signal.

The novel non-isotherm al reaction method of the invention provides asubstantial improvement over existing isothermal and thermal cyclingconditions. By favouring enzyme activity and optimal reaction kineticsthe method has improved the change in A_(T), increased the total amountof fluorescence generated, improved the consistency of amplification andincreased the sensitivity of detection.

Example 3: Results Using SYBR Green II

Because molecular beacons only measure an increase in the total amountof specific single-stranded DNA product, non-specific amplificationproduct is not measured independently of the intended amplificationproduct. To measure the production of non-specific amplificationproducts (e.g. arising from primer dimer formation), separate reactionswere carried out in the presence of SYBR Green II. SYBR Green II is oneof the most sensitives dyes known for detecting single-stranded DNA,RNA, and double-stranded DNA. Because SYBR Green II has a low intrinsicfluorescence, it is a natural choice for detection of totalamplification in a reaction or non-specific amplification if theamplification is done in the presence of no target. The reactions werecarried out directly under two conditions, isothermal and non-isothermal(STAR) as displayed below in Table 2.

TABLE 2 Temperature Preincubation Start Decrease Finish IsothermalConditions 56° C. 56° C. none 56° C. STAR Conditions 60° C. 60° C. −1.0°C. per minute 51° C.

Further, the reactions compared 50 copies of genomic DNA versus notarget. SYBR Green II was acquired at a 10,000× concentration, 0.Sx wasused per reaction (Life Technologies, Carlsbad). A higher TL, 9000, wasused to calculate the Ar due to the intrinsic nature of intercalatingdyes. SYBR Green II has an inverse relationship of fluorescence totemperature. The lower the temperature the higher the fluorescentsignal, as described in “Comparison of multiple DNA dyes for real-timePCR: effects of dye concentration and sequence composition on DNAamplification and melting temperature” (Gudnason et al., 2007 Nucl.Acids Res. 35 (19) e127). The results are shown in Table 3 below.

TABLE 3 SYBR ® Green II Reactions Isothermal Conditions Differencebetween Target to Average A_(T) No Target Target (minutes) Amplification50 copies gDNA 3.75 0.25 No Target 4 STAR Conditions Average A_(T)Target (minutes) 50 copies gDNA 3 1 No Target 4

The STAR method exhibits multiple improvements; first it reducesbackground production which is evident by the longer time it takes forthe “no target” to show SYBR Green II amplification relative to targetsignal. Secondly, it has improved product amplification, seen by thefaster amplification time when target is present. Combined, theseimprovements more than quadruple the difference between the AT relativeto isothermal methods.

It should be noted that AT values from isothermal reactions had morevariability than AT values from STAR. This shows the benefit that thenew method has in controlling the amplification process and reflects theunpredictability of non-specific amplification pathways usingtraditional methods.

Example 4: Results Using 2′ O-Methyl Modified Primers

As described in U.S. Pat. Nos. 6,794,142 and 6,130,038, the use of 2′O-methyl modified primers are known to reduce primer dimer formationduring amplification. US 2005-0059003 describes the use of 2′ O-methylmodifications located at the 3′ of SDA primers, thus Bst DNA PolymeraseI and derivatives can efficiently utilize 2′-modified ribonucleotides asprimers for DNA synthesis. Target specific primer regions comprising oneor more 2′ modified nucleotides (e.g., 2′-O-methyl, 2′-methoxyethoxy,2′-fluoro, 2′-allyl, 2′-O-[2(methylamino)-2-oxoethyl], 2′-hydroxyl(RNA), 4′-thio, 4′-CH3-O-2′-bridge, 4′-(CH3) 3-O-2′-ridge, 2′-LNA, and2′-O—(N-methylcarbamate 2′-Suc-OH)) should improve isothermal reactions.If 2′ modified nucleotides fully eliminated primer dimer formation itwould be surprising that the STAR method could further improveamplification. The reactions were carried out directly between twoconditions, isothermal and non-isothermal (STAR) as displayed below

TABLE 4 Temperature preincubation Start Decrease Finish IsothermalConditions 56° C. 56° C. none 56° C. STAR Conditions 60° C. 60° C. −1.0°C. per minute 51° C.

The results of amplification using 2′ modified nucleotides on the 3′ endof primers are shown in table 5 below. Reactions were carried out with aminimum of six replicates in no target reactions and twelve replicateswith target reactions.

TABLE 5 SYBR ® Green II Reactions 2′ O-methyl modifications IsothermalConditions Difference between Target to Average A_(T) No Target Target(minutes) Amplification 50 copies gDNA 5 0.5 No Target 5.75 STARConditions Average A_(T) Target (minutes) 50 copies gDNA 4 1.5 No Target5.5

The data demonstrate that the use of at least one primer incorporating2′ O-methyl nucleotides delays the formation of primer dimers improvingthe reaction, albeit slowing it down Further, the use of the STAR methodnot only improved the use of 2′ O-methyl amplification, recovering someof the lost speed, but also improved the difference between target to notarget amplification by three fold This indicates that although 2′O-methyl modifications do reduce the production of non-specific, errant,amplification they do not eliminate it. The data further suggest thatthe STAR method better utilizes the improvements generated by 2′O-methyl modifications than existing techniques previously disclosed.

Without limiting the invention to any particular theory, the potentialimprovements obtained by using one or more 2′ modified nucleotide in theprimer region are hypothesized to be largely due to enhancements in theinitiation phase of amplification. During the initial extension of theprimer region on a target the incorporation of one or more 2′ modifiednucleotides in the primer region of STAR causes these nucleotides to beunsuitable to serve as template for polymerase extension in nonspecificcomplexes fanned by interactions of primers, reducing the backgroundsignal. It is quite possible that the polymerase stalls as thenucleotide enters the binding pocket. In non-productive reactions (i.e.,off-target or primer dimer formation), the stalling effect is sufficientin minimizing aberrant extension because template binding is near itsmelting temperature.

Consequently, 2′ modifications are able to: restrict undesirableamplification pathways because the reaction has mired. However, duringfavourable amplifications, 2′ modifications reduce melting temperaturesthus negatively affecting amplification, slowing down time loamplification. STAR is able to take advantage of 2′ modifications whileminimizing the negative target amplification drawbacks.

This polymerase stalling further explains why STAR in conjunction with2′ O-methyl modifications improve each other. The initial increase intemperature found in the STAR method, besides naturally reducing primerdimers, exacerbates the 2′ modification stalling and melting of primersbefore errant amplification can occur, thus both methods complement oneanother. Furthermore, since STAR involves reducing temperature, thedecreases in melting temperature caused by 2′ modifications in theprimers can be minimized as the reaction proceeds.

Example 5: Results Using Multiple Polymerases

Existing amplification technologies either thermally cycle or run atconstant temperature. The method of the present invention does neitherbut rather runs by decreasing the temperature without cycling. Aparticular novel feature of the invention is the ability to use enzymesof similar function but with different temperature optima. For example,this technology will allow for the use of multiple primers designed fornicking endonucleases that function at different temperature optima,along with different strand displacement polymerases with differentoptima. Without limiting the invention to any particular theory, thismethod opens up rapid amplification methods, allowing for newcombinations of enzymes and primers not seen in existing technologies.The reactions below (Table 6) were carried out directly between threeconditions, isothermal, non-isothermal (STAR), and non-isothermal (STAR)with BSU polymerase (in addition to the initial Manta 1.0 polymerase) asdisplayed below. BSU Polymerase was purchased from New England BioLabs(Ipswich, MA) and ran at 0.5U per reaction. All conditions were runusing 18 target replicates and 6 no target replicates.

TABLE 6 preincubation Start Temperature Decrease Finish IsothermalCondition 56° C. 56° C. none 56° C. STAR Condition 60° C. 60° C. −0.5°C. per 15 seconds 40° C. STAR Condition + BSU Polymerase 60° C. 60° C.−0.5° C. per 15 seconds 40° C.

The amplification reactions were performed using samples containing 10copies of C. trachomatis genomic DNA, and the results are shown in FIGS.12A-12C.

FIG. 12A shows the results for the isothermal reaction (not inaccordance with the invention). FIG. 12B shows the results for the STARreaction in the presence of Manta polymerase alone, and FIG. 12C showsthe results for the STAR reaction in the presence of additional BSUpolymerase.

The first obvious difference is the lack of detection of 10 copies ofgenomic DNA by the isothermal method, only 9 of 18 replicates exceededthe fluorescence threshold-level (TL) and could be said to haveamplified. Both STAR methods detected 17 of 18 replicates. (It should benoted that the missed replicate in each STAR method was due to a faultymultichannel pipette).

Although the differences between the STAR methods are less stark, theaddition of a second polymerase with a lower optimal temperature, 37°C., improved total fluorescence after 10 minutes. Further, the secondpolymerase also tightens the replicates, decreasing A_(T) variability.This difference would be further demonstrated if a commercial stranddisplacement polymerase was available on the market with a temperatureoptimum at 45° C. to 50° C. The results indicate that the STAR method issuperior to the isothermal condition and further that this technologyallows for novel new mechanics, enzyme combinations and primeramplification schemes.

Example 6: Reproducibility

For validation of the consistency of STAR technology a large replicatestudy, vas carried out comparing STAR and published isothermalconditions as described in U.S. Pat. No. 9,562,263. Amplifications, STARvs Isothermal, were carried out using 100 plus replicates for reactionscontaining target and 16 replicates for control reaction mixtureswithout target. Both conditions used the same buffers, polymerase,nicking enzyme and target As shown in the scatter plot in FIG. 13 , theSTAR technology shows a dear improvement in average time (A_(T)) toachieve amplification to threshold level of fluorescence (TL), improvedsensitivity, and a reduced standard deviation between replicates. TheA_(T) time for reactions performed according to the invention was 3.35minutes, whilst the A_(T) value for reactions performed according toconventional isothermal protocols was 4.88 minutes, a difference whichis statistically significant as judged by Two-tailed t-test. Not tolimit the applicant to any particular theory, the significant reductionin amplification time is thought to be due to the improved initiation ofthe reaction, allowing for more efficient low copy amplification,minimized primer dimer events, and increased specific product extensionsgenerate templates faster than previously disclosed methods.

Example 7: Amplification Reactions Performed Beyond ConventionalIsothermal Temperature Ranges

A further benefit of STAR technology is the ability to amplify outsidemost common isothermal amplification temperature ranges. As described inU.S. Pat. Nos. 5,712,124, 9,562,263, and 5,399,391, most isothermalamplification technologies have a tight temperature range in whichamplification can occur. Outside these typical temperature ranges,conventional isothermal techniques have difficulty amplifying. Todemonstrate the versatility of STAR, amplifications were carried out asdescribed in Table 7 below.

TABLE 7 Isothermal Conditions Temper- pre- ature incubation StartDecrease Finish 63° C. 63° C. none 63° C. 49° C. 49° C. none 49° C. STARConditions 1^(st) Temper- pre- ature incubation Start Decrease 1^(st)Stop 62° C. 62° C. −0.8° C. 32° C. per 15 seconds 63° C. 63° C. −0.8° C.33° C. per 15 seconds 64° C. 64° C. −0.9° C. 28° C. per 15 seconds TwoStep STAR Conditions 1^(st) Drop 2^(nd) Temper- Imme- Temper- pre- ature1^(st) diately ature incubation Start Decrease Stop restart DecreaseFinish 63° C. 63° C. −0.8° C. 60° C. 49° C. −0.2° C. 42° C. per 15 per15 seconds seconds One Step STAR then Isothermal Conditions 1^(st) Drop2^(nd) Temper- Imme- Temper- pre- ature 1^(st) diately ature incubationStart Decrease Stop restart Decrease Finish 63° C. 63° C. −0.8° C. 60°C. 49° C. none 49° C. per 15 seconds

Isothermal reactions were performed as described in U.S. Pat. No.9,562,263. FIGS. 14A and 14B are graphs showing the amount offluorescence signal (background subtracted; arbitrary units) againsttime (minutes) for isothermal amplification reactions performed ateither 63° C. (FIG. 14A) or 49° C. (FIG. 14B). In both Figures, thedotted plots represent the results obtained from negative controlreactions without template; the solid line plots are the results fromthe test reactions containing template.

It is clear from FIG. 14A that substantially no template-specificamplification occurs when the reaction temperature is held at 63° C. InFIG. 14B, the results appear to suggest that at 49° C. amplification isoccurring from about 9 minutes onwards, but actually this is probablyfalse signal arising from interactions of molecular beacons with primers(data not shown).

In contrast to the isothermal reactions, “STAR” reactions performed inaccordance with the invention could be initiated at elevatedtemperatures and still achieve good amplification. The results fromthese reactions are shown in FIGS. 15A, B and C. These are graphs offluorescence (background subtracted, arbitrary units) against time(minutes). The solid shading indicates the temperature (° C.) during thereactions. The dotted plots represent the results obtained using 10copies of target, the solid plots represent the results obtained using100 copies of target. In FIG. 15A, the initial temperature was 62° C.,and the rate of temperature decrease was −0.8° C. per 15 seconds (i.e.−3.2° C. per minute). In FIG. 15B, the initial temperature was 63° C.,and the rate of temperature decrease was −0.8° C. per 15 seconds. InFIG. 15C, the initial temperature was 64° C., and the rate oftemperature decrease was −0.9° C. per 15 seconds (i.e. −3.6° C. perminute). It is apparent from the Figures that an initial temperature of62 or even 63° C. provides good results for STAR reactions, and there iseven some amplification using an initial temperature of 64° C. althoughthis is clearly sub-optimal.

In addition, experiments were performed using large temperature drops.The results are shown in FIGS. 16A and 16B. The graphs show the resultsfor no target negative controls (no fluorescence signal above thresholdlevel) and for STAR reactions performed in the presence of 10 or 100copies of target C. trachomatis genomic DNA.

FIG. 16A shows the results obtained using an initial temperature of 63°C., followed by a temperature reduction rate of −0.8° C. per 15 secondsfor 1 minute, followed by a sudden reduction to 49° C., and then agradual temperature reduction of −0.2° C. per 15 seconds (i.e. −0.8° C.per minute) for the duration of the reaction. The graph shows thatamplification was achieved for both 10 and 100 copy number reactions,although there was approximately twice as much fluorescence signal forthe 100 copy target reactions compared to the 10 copy target reactions,and there was considerable intra-group variability.

FIG. 16B shows the results obtained using the same 63° C. initialtemperature for 1 minute, followed by the sudden reduction to 49° C.Thereafter, the reaction temperature was held at 49° C. for the durationof the experiment. It can be seen from the graph that there is goodspecific amplification and much less intra-group variation (reactionsperformed with 100 copy number target or no target only).

The ability of STAR to amplify across a 40° C. temperature range clearlyindicates that STAR is very different from conventional amplificationreactions. Atypical reaction temperatures with large ranges are unusualand would not be expected to work. Not to limit the applicant to anyparticular theory, it is unexpected that these large temperature rangesseem to be less restrictive on amplification for STAR than forconventional amplification methods. Possibly the ability of STAR toachieve superior amplification across a larger range of temperatures isdue to improving primer specificity and binding along with strategicallyutilizing enzyme temperature optima. By utilizing a higher temperaturefor the initiation phase, one favours true product amplification andthus improves the efficiency of all subsequent phases, exponentialamplification and detection. This selection and subsequent temperaturedrop opens up the amplification toolbox as new schemas for enzymes,primers, and temperatures can be realized.

Example 8: Results Using Six- and Seven-2′-O-Methyl

As previously described, 2′-O-methyl modified primers are known toreduce primer dimer formation during amplification. Further illustratingthe cooperative nature of these modifications with the STAR technologyis the ability to incorporate large strings of 2′-O-methyl modificationsand still achieve amplification. Typically, 2′-O-methyl modificationsstall the polymerase, permanently retarding amplification; six or moreis believed to cause the polymerase to “fall off” the complex ratherthan just stall. FIGS. 17A and 17B demonstrate STAR's ability totolerate these modifications and achieve significant amplification withlonger 2′-O-methyl strings than previously identified. The structure ofthe primers containing 2′-O-methylated bases is shown in FIGS. 1B and1C.

FIGS. 17A and 17B are graphs of (background-subtracted) fluorescence(arbitrary units) against time (minutes). The shading indicates thetemperature profile (° C.) over time during the course of theamplification reactions. FIG. 17A shows the results for reactionsperformed using primers containing 6 2′-O-methyl modified bases, andFIG. 17B shows the results for reactions performed using 7 2′-O-methylmodified bases. In both cases, no target negative control reactions didnot generate any fluorescence signal, whereas there was goodamplification using either of the modified primers, although the averagefluorescence signal was slightly higher for the 6 modified base primers,and the intra-group variation was considerably less compared to theresults from the 7 modified base primers.

As seen in the figures, primers containing strings of six and seven 2′O-methyl's amplify well with STAR. This could be due to the ability ofSTAR to begin amplification in the highly favourable temperature regionsof strand displacement polymerases, around 65° C. This favourable regionmay allow the polymerase to extend longer 2′ modified strings allowingfor initiation that other technologies lack. For brevity data is notshown but it can also be described that the full length of primerregions have been modified with 2′-O-methyl's and shown amplification,although slower and with lower fluorescent signal.

Example 9: Results Using Ribonucleic Acid

STAR can amplify from any nucleic acid, using any composition of DNA(cDNA and gDNA), RNA (mRNA, tRNA, rRNA, siRNA, microRNA), RNA/DNAanalogs, sugar analogs, hybrids, polyamide nucleic acid, and other knownanalogs. Amplification of ribosomal RNA was carried out as describedbelow.

Enzymes, Oligonucleotides, and Target:

Listeria monocytogenes was used as the target for the development of theSTAR RNA assay. Listeria monocytogenes (ATCC VR-886) genomic DNA wasacquired from American Type Culture Collection (Manassas, VA). Initialscreening was performed on gDNA, and a 23S region of ribosomal RNA wasfound to be amplified with primers LMONF72 (SEQ ID NO: 4,5′-GGACTCGATATCGAGTCCAGTTACGATTTGTTG-3′) and LMONR86 (SEQ ID NO: 5,5′-gGACTCCATATGGAGTCCTACGGCTCCGCTTTT-3′). The resulting DNA template wasdetected using a molecular beacon LMONMB1 (SEQ ID NO: 6,5′-FAM/gctgcGTTCCAATTCGCCTTTTTCGCagc/BHQI-3′) as described in EP No.0728218. Total RNA was isolated using the RNeasy Plus mini kit Qiagen(Hilden, Germany) combined with rapid mechanical lysis on a Mini BeadMill 4 (VWR). Listeria monocytogenes (ATCC BAA-2660) was acquired fromAmerican Type Culture Collection (Manassas, VA), and revived by platingon brain-heart infusion agar plates (BHI). A single colony was used toinoculate 25 mL of BHI media that was grown for 18 hours at 37° C. toreach stationary phase. The culture was then back-diluted and grown foran additional four hours prior to harvest. Bacteria pellets wereresuspended in RLT lysis buffer, and homogenised on the Mini Bead Mill(VWR). Total RNA was purified per manufacturer's directions (Qiagen).Genomic DNA was removed by passing lysates over a DNA-binding columnprovided in the RNeasy Plus purification kit. Genomic DNA contaminationwas further minimized by an on-column DNAse I digestion of samples onthe RNeasy RNA-binding column. Bst X DNA Polymerase was purchased fromBeverly Qiagen (Beverly, MA). Omniscript, a Reverse Transcriptase, waspurchased from Qiagen (Hilden, Germany). Nt.BstNBI nicking endonucleasewas purchased from New England BioLabs (Ipswich, MA) as described inU.S. Pat. No. 6,191,267. Oligonucleotides and molecular beacons weresynthesized by Integrated DNA Technologies (Coralville, IA).

Amplification Conditions

The basic STAR mixture contained everything as described in example 1above with the

1. A method of performing a non-isothermal nucleic acid amplificationmethod comprising: (a) incubating a reaction mixture comprising a targetnucleic acid and one or more complementary single stranded primers at afirst temperature, T1, which permits a hybridisation event in which theone or more primers hybridize to the target, which hybridisation event,directly or indirectly, leads to the formation of a duplex structurecomprising two nicking sites disposed at or near opposite ends of theduplex; (b) cooling the temperature of the reaction mixture to a secondtemperature, T2, which is at least 2° C. lower than T1; (c) using anicking enzyme to cause a nick at each of said nicking sites in thestrands of the duplex; (d) using a polymerase to extend the nickedstrands so as to form newly synthesized nucleic acid, which extensionwith the polymerase creates nicking sites; (e) repeating steps (c) and(d) so as to cause the production of multiple copies of the newlysynthesized nucleic acid; wherein after step (b), the temperature doesnot return to the first temperature. 2.-31. (canceled)
 32. The method ofclaim 1, wherein the cooling is by application of active cooling to thereaction mix.
 33. The method of claim 1, wherein the cooling is achievedby passive means.
 34. The method of claim 1, wherein the cooling isachieved by a combination of active and passive means.
 35. The method ofclaim 1, wherein the reaction mix is cooled during step (b) by at least15° C.
 36. The method of claim 1, wherein the temperature T1 in step (a)is in the range 55-62° C.
 37. The method of claim 1, wherein steps(b)-(e) are performed substantially immediately after step (a), andwherein steps (a)-(e) are performed in the same reaction vessel or onthe same solid support.
 38. The method of claim 1, wherein step (c) isinitiated by formation of the duplex structure which comprises twonicking sites disposed at or near opposite ends of the duplex.
 39. Themethod of claim 1, further comprising a step of contacting a mixtureobtained by performance of the method with a thermolabile enzyme whichdegrades nucleic acids, the mixture being contacted with thethermolabile enzyme at a temperature at which the thermolabile enzyme issubstantially active.
 40. The method of claim 1, further comprising astep of directly or indirectly detecting the newly synthesized nucleicacid.
 41. The method of claim 1, wherein step (e) is performed whilefurther cooling the reaction mix.
 42. The method of claim 41, whereinthe reaction mix is cooled during step (b) and/or step (e) by at least15° C.
 43. The method of claim 41, wherein the cooling is by applicationof active cooling to the reaction mix.
 44. The method of claim 41,wherein the cooling is achieved by passive means.
 45. The method ofclaim 41, wherein the cooling is achieved by a combination of active andpassive means.
 46. The method of claim 41, wherein the temperature T1 instep (a) is in the range 55-62° C.
 47. The method of claim 41, whereinsteps (b)-(e) are performed substantially immediately after step (a),and wherein steps (a)-(e) are performed in the same reaction vessel oron the same solid support.
 48. The method of claim 41, comprising use ofa first polymerase and/or a first nicking enzyme having an optimumtemperature, and a second polymerase and/or a second nicking enzymehaving an optimum temperature, wherein the optimum temperature of thesecond polymerase and/or second nicking enzyme is lower than the optimumtemperature of the respective first polymerase and/or first nickingenzyme.
 49. The method of claim 41, further comprising the step ofcontacting a mixture obtained by performance of the method with athermolabile enzyme which degrades nucleic acid, the mixture beingcontacted with the thermolabile enzyme at a temperature at which thethermolabile enzyme is substantially active.
 50. The method of claim 41,further comprising a step of directly or indirectly detecting the newlysynthesized nucleic acid.